Several bacteria use the plant hormone indole-3-acetic acid (IAA) as a sole carbon and energy source. A cluster of genes (named iac) encoding IAA degradation has been reported in Pseudomonas putida 1290, but the functions of these genes are not completely understood. The plant-growth-promoting rhizobacterium Paraburkholderia phytofirmans PsJN harbors iac gene homologues in its genome, but with a different gene organization and context than those of P. putida 1290. The iac gene functions enable P. phytofirmans to use IAA as a sole carbon and energy source. Employing a heterologous expression system approach, P. phytofirmans iac genes with previously undescribed functions were associated with specific biochemical steps. In addition, two uncharacterized genes, previously unreported in P. putida and found to be related to major facilitator and tautomerase superfamilies, are involved in removal of an IAA metabolite called dioxindole-3-acetate. Similar to the case in strain 1290, IAA degradation proceeds through catechol as intermediate, which is subsequently degraded by ortho-ring cleavage. A putative two-component regulatory system and a LysR-type regulator, which apparently respond to IAA and dioxindole-3-acetate, respectively, are involved in iac gene regulation in P. phytofirmans. These results provide new insights about unknown gene functions and complex regulatory mechanisms in IAA bacterial catabolism.IMPORTANCE This study describes indole-3-acetic acid (auxin phytohormone) degradation in the well-known betaproteobacterium P. phytofirmans PsJN and comprises a complete description of genes, some of them with previously unreported functions, and the general basis of their gene regulation. This work contributes to the understanding of how beneficial bacteria interact with plants, helping them to grow and/or to resist environmental stresses, through a complex set of molecular signals, in this case through degradation of a highly relevant plant hormone.KEYWORDS indole-3-acetic acid catabolism, iac genes, Paraburkholderia phytofirmans, plant-growth-promoting rhizobacteria I ndole-3-acetic acid (IAA) belongs to a class of plant hormones called auxins, which play a key role in plant growth and development, controlling cell division, elongation, differentiation, and tropism responses to gravity and light (1, 2). A crucial characteristic of auxin-mediated effects is related to the differential distribution of auxin in tissues (2); therefore, plants tightly control IAA levels through biosynthesis, conjugation, degradation, and intercellular transport (3). Aside from auxin being an essential molecule for

cCupriavidus pinatubonensis JMP134, like many other environmental bacteria, uses a range of aromatic compounds as carbon sources. Previous reports have shown a preference for benzoate when this bacterium grows on binary mixtures composed of this aromatic compound and 4-hydroxybenzoate or phenol. However, this observation has not been extended to other aromatic mixtures resembling a more archetypal context. We carried out a systematic study on the substrate preference of C. pinatubonensis JMP134 growing on representative aromatic compounds channeled through different catabolic pathways described in aerobic bacteria. Growth tests of nearly the entire set of binary combinations and in mixtures composed of 5 or 6 aromatic components showed that benzoate and phenol were always the preferred and deferred growth substrates, respectively. This pattern was supported by kinetic analyses that showed shorter times to initiate consumption of benzoate in aromatic compound mixtures. Gene expression analysis by real-time reverse transcription-PCR (RT-PCR) showed that, in all mixtures, the repression by benzoate over other catabolic pathways was exerted mainly at the transcriptional level. Additionally, inhibition of benzoate catabolism suggests that its multiple repressive actions are not mediated by a sole mechanism, as suggested by dissimilar requirements of benzoate degradation for effective repression in different aromatic compound mixtures. The hegemonic preference for benzoate over multiple aromatic carbon sources is not explained on the basis of growth rate and/or biomass yield on each single substrate or by obvious chemical or metabolic properties of these aromatic compounds.A romatic compounds (AC) are widespread in the environment, displaying a heterogeneous structural diversity. They can be naturally originated by biotic and abiotic processes or released as pollutants into the environment. AC primarily can be found as aromatic amino acids, secondary products abundantly generated by plants, structural components of the very complex lignin heteropolymer in woody plants, and xenobiotic compounds: biocides, industrial by-products, and petroleum derivatives, among others. Microorganisms may degrade hundreds of different AC using specialized biochemical pathways that allow them to grow on these carbon sources (1-3). Typically, bacteria deal with AC as part of complex mixtures in naturally occurring organic compounds, such as those found in plant exudates (4), in soils (5), and even in dissolved organic matter from freshwater and seawater (6). Therefore, microorganisms are concurrently exposed to several structurally heterogeneous AC as potential substrates, which raises the question of whether the components of these mixtures are used simultaneously or in a sequential manner. In the case of the sequential utilization pattern, characterized by diauxic growth, one compound inhibits degradation of the other by exerting metabolite toxicity (7), competitive inhibition of enzymes (8, 9), depletion of electron acceptors (10, 11),...